General information for g11872.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein suppressor of forked.
Parent gene
- The parent gene g11872 is located on chr_1: 18882825..18886305 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_1 | g11872 | g11872.t3 | TTS | g11872.t3 | 18880028 | 18880028 |
| chr_1 | g11872 | g11872.t3 | isoform | g11872.t3 | 18880104 | 18882755 |
| chr_1 | g11872 | g11872.t3 | exon | g11872.t3.exon1 | 18880104 | 18880321 |
| chr_1 | g11872 | g11872.t3 | cds | g11872.t3.CDS1 | 18880104 | 18880321 |
| chr_1 | g11872 | g11872.t3 | exon | g11872.t3.exon2 | 18880389 | 18880493 |
| chr_1 | g11872 | g11872.t3 | cds | g11872.t3.CDS2 | 18880389 | 18880493 |
| chr_1 | g11872 | g11872.t3 | exon | g11872.t3.exon3 | 18880646 | 18881345 |
| chr_1 | g11872 | g11872.t3 | cds | g11872.t3.CDS3 | 18880646 | 18881345 |
| chr_1 | g11872 | g11872.t3 | exon | g11872.t3.exon4 | 18881410 | 18881601 |
| chr_1 | g11872 | g11872.t3 | cds | g11872.t3.CDS4 | 18881410 | 18881601 |
| chr_1 | g11872 | g11872.t3 | exon | g11872.t3.exon5 | 18882010 | 18882070 |
| chr_1 | g11872 | g11872.t3 | cds | g11872.t3.CDS5 | 18882010 | 18882070 |
| chr_1 | g11872 | g11872.t3 | exon | g11872.t3.exon6 | 18882129 | 18882259 |
| chr_1 | g11872 | g11872.t3 | cds | g11872.t3.CDS6 | 18882129 | 18882259 |
| chr_1 | g11872 | g11872.t3 | exon | g11872.t3.exon7 | 18882316 | 18882483 |
| chr_1 | g11872 | g11872.t3 | cds | g11872.t3.CDS7 | 18882316 | 18882483 |
| chr_1 | g11872 | g11872.t3 | exon | g11872.t3.exon8 | 18882536 | 18882755 |
| chr_1 | g11872 | g11872.t3 | cds | g11872.t3.CDS8 | 18882536 | 18882709 |
| chr_1 | g11872 | g11872.t3 | TSS | g11872.t3 | 18883566 | 18883566 |
Sequences
>g11872.t3 Gene=g11872 Length=1795
AGAGAAACTGGCACAAGCATACGATTTTGCACTTGAAAAAATTGGAATGGATCTTCATTC
ATATTCAATTTGGTCGGACTATATTGTATTTCTAAAAAGTTTTGAACCTATTGGTAGTTT
TGCGGAAAATCAACAAATTACTGCTATTCGAAGGGTTTATCAAAAAGCGGTTCTTACGCC
AATAATCGGAATCGAAGTTCTTTGGAAGGAGTATATACAGTTTGAGCACAAAATTAATCC
AGTTATTTCGGAAAAGATGAGTTTGGAACGATCTCGTGATTACATGAATGCACGTCGTGT
AGCAAAAGAACTTGAGCATATTACAAAAGGTTTGAACAAAAACTTACCAGCCGTTCAACC
TACTTTAACTAAAGAAGAATTTAAACAAGCTGAATTATGGAGAAAATTCATTAATTTTGA
AAAATCAAATCCTTTAAGAAGTGAAGATACAGCTCTCGTATCAAGACGAGTAATGTTTGC
AACTGAACAATGTCTACTTGTAATGTGTCATCATCCATCTTTCTGGATAATGGCCGCTCA
ATATTTGGACAGTACAGCTAAACATTTAACAGAGAAAGCAGATGTAAATGCAGCCAAAAT
ATTTTATGATGAAGTAGCAAATATACTTGAGAGAGCAATCAACGGTGTGATGAGTAGAAA
TACATTACTTTACTTTACATATACTGATTTCGAAGAAGGAAGATTAAAATATGAAAAAGT
CCATCAAATGTACAACAAATTTCTTGCTATACCCGATATCGATCCGACTTTGGTCTATGT
TCAATATATGAAGTTTACAAGAAGAGCAGAAGGAATTAAATCTGCTCGTGCCATATTCAA
ACGCGCAAGAGAAGATGTTCGTTCCCGATATCATGTTTTCGTAGCTGCTGCATTAATGGA
ATATTATTGCAGCAAAGATAAAGATATTGCATTTCGTATTTTCGAGTTAGGCTTGAAACG
ATTTGGAGGAAGTCCTGAATATGTTATGTGTTATATTGACTATTTATCTCATTTAAATGA
AGATAATAACACAAGAGTTCTCTTTGAAAGAGTTTTATCTTCTGGAGGTTTAACTAATCA
GCTTTCTGTGCAGATTTGGAATAAATTTTTAGAATTTGAATCAAACATTGGCGATTTGTC
ATCAATCGTGAAAGTAGAACGGCGTCGCAGTGCAGTTCTAGAAAATTTAAAAGAATACGA
AGGAAAGGAAACTGCACAATTGATTGATCGTTACAAGTTTTTGGATCTTTATCCTTGTAG
TCAAGCTGAACTGAAATCAGTTGGTTATTACGAAATATCATCCATCAGTAGTGGAGGACA
AAAAGTAGTCCAACAGAATCAAGAAGAAGAAGAATCTCAAAAAGTTCTTCCTCGTCCTGA
TTTTTCTCAGATGATTCCATTTAAGCCCAAGTCAAATGCATATCCTGGTGAACATCCAAT
GGGTAGTGGAGGCACTTTTCCGCAACCAATAGCTCTTGCGGCTCTCTGTGCAACTTTGCC
GCCACCAATTTGCTTTAGAGGACCATTTGTATCAGTTGATAAGCTGATTGATGTATTTAA
CCGAATCAAAATTGATGCACCTGTTCCATCTGAAAATGGCTTGGATACAAAATTGTTTGA
CCTTGCAAAATCTGTTCATTGGATTGTTGATGAAAGTCATCAATATGAAGGAATCAAAAG
AAGGAGAATTTTGCCAGGAGGTGGTGAAGACTCTGATGACGAAACAACAAATACTGCTAA
TCCACCAGTCAATGACATTTATCGTTTAAGACAACAAAAAAAATTTAATAAATAA
>g11872.t3 Gene=g11872 Length=582
MDLHSYSIWSDYIVFLKSFEPIGSFAENQQITAIRRVYQKAVLTPIIGIEVLWKEYIQFE
HKINPVISEKMSLERSRDYMNARRVAKELEHITKGLNKNLPAVQPTLTKEEFKQAELWRK
FINFEKSNPLRSEDTALVSRRVMFATEQCLLVMCHHPSFWIMAAQYLDSTAKHLTEKADV
NAAKIFYDEVANILERAINGVMSRNTLLYFTYTDFEEGRLKYEKVHQMYNKFLAIPDIDP
TLVYVQYMKFTRRAEGIKSARAIFKRAREDVRSRYHVFVAAALMEYYCSKDKDIAFRIFE
LGLKRFGGSPEYVMCYIDYLSHLNEDNNTRVLFERVLSSGGLTNQLSVQIWNKFLEFESN
IGDLSSIVKVERRRSAVLENLKEYEGKETAQLIDRYKFLDLYPCSQAELKSVGYYEISSI
SSGGQKVVQQNQEEEESQKVLPRPDFSQMIPFKPKSNAYPGEHPMGSGGTFPQPIALAAL
CATLPPPICFRGPFVSVDKLIDVFNRIKIDAPVPSENGLDTKLFDLAKSVHWIVDESHQY
EGIKRRRILPGGGEDSDDETTNTANPPVNDIYRLRQQKKFNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g11872.t3 | Coils | Coil | Coil | 367 | 387 | - |
| 13 | g11872.t3 | Gene3D | G3DSA:1.25.40.1040 | - | 1 | 412 | 2.8E-133 |
| 12 | g11872.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 546 | 572 | - |
| 11 | g11872.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 556 | 570 | - |
| 2 | g11872.t3 | PANTHER | PTHR19980 | RNA CLEAVAGE STIMULATION FACTOR | 1 | 580 | 2.0E-177 |
| 1 | g11872.t3 | Pfam | PF05843 | Suppressor of forked protein (Suf) | 241 | 509 | 9.6E-80 |
| 9 | g11872.t3 | SMART | SM00386 | hat_new_1 | 29 | 62 | 0.0057 |
| 4 | g11872.t3 | SMART | SM00386 | hat_new_1 | 95 | 127 | 46.0 |
| 6 | g11872.t3 | SMART | SM00386 | hat_new_1 | 185 | 218 | 110.0 |
| 5 | g11872.t3 | SMART | SM00386 | hat_new_1 | 220 | 253 | 54.0 |
| 10 | g11872.t3 | SMART | SM00386 | hat_new_1 | 255 | 287 | 56.0 |
| 8 | g11872.t3 | SMART | SM00386 | hat_new_1 | 290 | 322 | 0.74 |
| 7 | g11872.t3 | SMART | SM00386 | hat_new_1 | 324 | 360 | 0.022 |
| 3 | g11872.t3 | SUPERFAMILY | SSF48452 | TPR-like | 1 | 416 | 6.83E-111 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006397 | mRNA processing | BP |
| GO:0006396 | RNA processing | BP |
| GO:0005634 | nucleus | CC |
| GO:0005515 | protein binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
